Subthreshold transcranial magnetic stimulation (TMS) applied to the human motor cortex suppresses voluntarily generated EMG activity (Davey et al. 1994; Petersen et al. 2001). The onset latency of the suppression of the EMG activity is about 10 ms later than the short latency excitation produced by TMS at intensities above motor threshold. This difference in latency can suggest that TMS may be activating either inhibitory pathways with several synaptic connections or slowly conducting axons acting on the cortical cells which are responsible for the EMG activity, or secondly, that the voluntary EMG may be generated via slowly conducting descending pathways. Here we applied subthreshold TMS to the motor cortex in awake human subjects and investigated the effect on the firing probability of single motor units activated by volition. Single pulses of TMS were delivered at stimulus intervals of 1-3 s. Post stimulus time histograms were generated for each single motor unit (24 units from biceps brachii and 13 units from first dorsal interosseus, FDI) using 113-405 TMS pulses per unit.. A clear suppression of 5 biceps units was seen at a mean latency of 18.1 ms with subthreshold magnetic stimulation of the motor cortex. At higher stimulus intensities a short-latency excitation occurred at a mean latency of 14.1 ms. Thus, the mean latency difference between excitation and suppression was 4.0 ms for the biceps units and 2.9 ms for the FDI units. The firing probability of the motor units was reduced by approximately 40% in both muscles during the suppression of activity. Subthreshold stimulation depressed single motor unit activity a few milliseconds after the short-latency excitation that is seen at higher intensities of stimulation. This suggests that pathways with fast conduction velocity are part of the voluntary activation of single motor units and that the suppression by TMS occurs via inhibitory circuits within a few synapses of the cortical output cells.